This is just part of the process. ATF is a fickle master. I had two Form 3s filled out exactly the same way - one got approved, the other denied. I had a client get his Form 4 denied over silly BS that has nothing to do with the NFA registration process but the Examiner, who doesn't hold a law degree, was inventing his own opinions on trust law.

For the record, when I worked for an FFL in college, I once called ATF for an opinion on legal issues and got 3 different and conflicting answers from the agents I talked with (this is why all business with ATF should be conducted in email/writing).

You've got a lot of new hires just getting their feet wet with examining NFA apps, so there are bound to be some unjustified delays. Which is sad considering that the "normal" delay is almost a year now.